Abstract

Our long-term objective is to ascertain how protein conformation plays a role in biological function and in various diseases.
Our specific aims are to treat the role of basic physical forces, key interactions, key residues, as well as the role of conformation, with an improved coarse-grained UNRES model, in several biological systems related to specific diseases. We will also continue the development of our UNRES model of nucleic acids (NARES-2P) and merge UNRES and NARES-2P into a viable package, which will be provided to the community. We will demonstrate how these aims can lead to valid predictions of structures and folding pathways of proteins, and protein-nucleic acid and protein-protein complexes. Our main focus will involve the application of this methodology to specific biological problems.

Public Health Relevance

As pointed out in the Project Summary, the long-term objective of this research is to ascertain how protein conformation plays a role in various diseases. Examples of such diseases in which conformation plays a role are sickle cell anemia and amyloid diseases such as Alzheimer's and mad cow disease.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM014312-58
Application #
8694188
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Wehrle, Janna P
Project Start
1977-01-01
Project End
2018-02-28
Budget Start
2014-06-02
Budget End
2015-02-28
Support Year
58
Fiscal Year
2014
Total Cost
$497,534
Indirect Cost
$172,533

  Institution

Name
Cornell University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850

  Publications

Cote, Yoann; Delarue, Patrice; Scheraga, Harold A et al. (2018) From a Highly Disordered to a Metastable State: Uncovering Insights of ?-Synuclein. ACS Chem Neurosci 9:1051-1065
Vorobjev, Yury N; Scheraga, Harold A; Vila, Jorge A (2018) A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris. J Biomol Struct Dyn 36:3094-3105
Grassein, Paul; Delarue, Patrice; Scheraga, Harold A et al. (2018) Statistical Model To Decipher Protein Folding/Unfolding at a Local Scale. J Phys Chem B 122:3540-3549
Solé-Domènech, Santiago; Rojas, Ana V; Maisuradze, Gia G et al. (2018) Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar A? by multiple endoproteolytic cleavages within the ?-sheet domain. Proc Natl Acad Sci U S A 115:1493-1498
Vorobjev, Yury N; Scheraga, Harold A; Vila, Jorge A (2018) Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins. J Biomol Struct Dyn 36:561-574
Keasar, Chen; McGuffin, Liam J; Wallner, Björn et al. (2018) An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Sci Rep 8:9939
Rojas, Ana; Maisuradze, Nika; Kachlishvili, Khatuna et al. (2017) Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics. ACS Chem Neurosci 8:201-209
He, Yi; Maisuradze, Gia G; Yin, Yanping et al. (2017) Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. Proc Natl Acad Sci U S A 114:1578-1583
Makowski, Mariusz; Liwo, Adam; Scheraga, Harold A (2017) Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. J Phys Chem B 121:379-390
Vila, Jorge A; Scheraga, Harold A (2017) Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH. J Mol Struct 1134:576-581

Showing the most recent 10 out of 86 publications